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 Post subject: Inconsistency in GPF
PostPosted: Mon May 19, 2014 11:43 pm 
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Joined: Wed May 14, 2014 5:57 pm
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Hi -

I am a new user of AutoDock Tools. I am trying to set up the docking of a Zn protein (including the Zn site) with a ligand.
I see the GPF and realized that the receptor and ligand types are not the same as the atom-specific affinity types. Should this be the reason why when I start autogrid, I get error messages?

How can I reconcile this difference?

Sincerely
Jayashree
Jayashree_sriniv@hotmail.com


------- 1qib.gpf -------

npts 40 44 44 # num.grid points in xyz
gridfld 1qib_clean.maps.fld # grid_data_file
spacing 0.994444444444 # spacing(A)
receptor_types A C HD N NA OA SA ZN # receptor atom types
ligand_types A C HD OA N # ligand atom types
receptor 1qib_clean.pdbqt # macromolecule
gridcenter 72.999 27.078 20.843 # xyz-coordinates or auto
smooth 0.5 # store minimum energy w/in rad(A)
map 1qib_clean.A.map # atom-specific affinity map
map 1qib_clean.C.map # atom-specific affinity map
map 1qib_clean.HD.map # atom-specific affinity map
map 1qib_clean.OA.map # atom-specific affinity map
map 1qib_clean.N.map # atom-specific affinity map
elecmap 1qib_clean.e.map # electrostatic potential map
dsolvmap 1qib_clean.d.map # desolvation potential map
dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant


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